SMTL ID : 9mul.1

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1, Glycine and Glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 10 residues within 4Å: Chain A: F.106, P.138, L.139, T.140, R.145, S.193, S.194, W.237, D.238, F.264 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:P.138, A:T.140, A:T.140, A:S.194, A:S.194, A:D.238, G.1 Water bridges: A:D.238 Salt bridges: A:R.145

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 10 residues within 4Å: Chain B: H.99, S.125, L.126, T.127, R.132, G.183, S.184, T.185, Y.225, D.226 14 PLIP interactions: 12 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.225 Hydrogen bonds: B:T.127, B:T.127, B:T.127, B:S.184, B:T.185, B:T.185, B:D.226, E.2, E.2 Water bridges: B:S.125, B:T.179 Salt bridges: B:H.99, B:R.132

1 x 01: 5-[(3-chlorobenzene-1-sulfonyl)methoxy]-6-methyl-N-[(pyridin-3-yl)methyl]pyrazine-2-carboxamide

01.3: 16 residues within 4Å: Chain A: I.141, P.154, Y.157, R.261, S.262, G.263 Chain B: V.140, P.141, F.142, V.143, E.144, L.275, V.278, M.283, E.287, L.291 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.141, B:F.142, B:E.287, B:L.291 Hydrogen bonds: B:F.142, B:E.144, A:R.261 pi-Stacking: A:Y.157 pi-Cation interactions: A:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bischoff, F.P. et al., Design, Synthesis, and Characterization of GluN2A Negative Allosteric Modulators Suitable for In Vivo Exploration. J.Med.Chem. (2025)

Release Date

2025-03-05

Peptides

Glutamate receptor ionotropic, NMDA 1: A
Glutamate receptor ionotropic, NMDA 2A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2A

Related Entries With Identical Sequence